Indexing failures in a few studies

[jimallman]

Today I used the deployment script to re-index oti, and a few studies failed (details below).

Study ot_232 reports multiple records(?) found, but there's just one JSON with this id in phylesystem-1. This is very similar to a problem discussed in #26:

Indexing http://api.opentreeoflife.org/phylesystem/v1/../ study ot_232 from http://api.opentreeoflife.org/phylesystem/v1/../default/v1/study/ot_232.json
Calling "http://127.0.0.1:7478/db/data/ext/studies/graphdb/index_studies" with data="{'urls': ['http://api.opentreeoflife.org/phylesystem/v1/../default/v1/study/ot_232.json']}"

Indexing failed for URL "http://api.opentreeoflife.org/phylesystem/v1/../default/v1/study/ot_232.json", study http://api.opentreeoflife.org/phylesystem/v1/../default/v1/study/ot_232.json. Message = "More than one hit found for ot:studyId == ot_232. The database is probably corrupt."

Two others failed with no explanation:

Indexing http://api.opentreeoflife.org/phylesystem/v1/../ study ot_31 from http://api.opentreeoflife.org/phylesystem/v1/../default/v1/study/ot_31.json
Calling "http://127.0.0.1:7478/db/data/ext/studies/graphdb/index_studies" with data="{'urls': ['http://api.opentreeoflife.org/phylesystem/v1/../default/v1/study/ot_31.json']}"

Indexing failed for URL "http://api.opentreeoflife.org/phylesystem/v1/../default/v1/study/ot_31.json", study http://api.opentreeoflife.org/phylesystem/v1/../default/v1/study/ot_31.json. Message = "null"

Indexing http://api.opentreeoflife.org/phylesystem/v1/../ study ot_32 from http://api.opentreeoflife.org/phylesystem/v1/../default/v1/study/ot_32.json
Calling "http://127.0.0.1:7478/db/data/ext/studies/graphdb/index_studies" with data="{'urls': ['http://api.opentreeoflife.org/phylesystem/v1/../default/v1/study/ot_32.json']}"

Indexing failed for URL "http://api.opentreeoflife.org/phylesystem/v1/../default/v1/study/ot_32.json", study http://api.opentreeoflife.org/phylesystem/v1/../default/v1/study/ot_32.json. Message = "null"

[snacktavish]

Indexing is failing for some studies.
For example, https://tree.opentreeoflife.org/curator/study/view/pg_2739 does not appear in the curator home, nor is findable by search. Also true for https://tree.opentreeoflife.org/curator/study/view/pg_761, the second study on the list of synthesis inputs.

[mtholder]

The cURL call that fails to return the studies for the list is:

curl 'https://api.opentreeoflife.org/oti/v1/findAllStudies' -H 'Origin: https://tree.opentreeoflife.org' -H 'Accept-Encoding: gzip, deflate' -H 'Accept-Language: en-US,en;q=0.8' -H 'User-Agent: Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/43.0.2357.81 Safari/537.36' -H 'Content-Type: application/x-www-form-urlencoded; charset=UTF-8' -H 'Accept: application/json, text/javascript, */*; q=0.01' -H 'Cache-Control: max-age=0' -H 'Referer: https://tree.opentreeoflife.org/curator' -H 'Connection: keep-alive' --data 'verbose=true' --compressed

(via copying the call form the chrome dev tools that is loading the curator).

[kcranston]

@chinchliff @blackrim Any idea what is going on here? Is this the same (or similar) problem as discussed here? Currently, not all of the studies in the synthetic tree are showing up in the curator app.

[chinchliff]

I am not sure what is going on. What errors are returned when indexing is
attempted for those studies?

On Mon, Jun 15, 2015 at 12:15 PM Karen Cranston notifications@github.com
wrote:

@chinchliff https://github.com/chinchliff @blackrim
https://github.com/blackrim Any idea what is going on here? Is this the
same (or similar) problem as discussed here
#26 (comment)?
Currently, not all of the studies in the synthetic tree are showing up in
the curator app.

—
Reply to this email directly or view it on GitHub
#34 (comment).

[jimallman]

@chinchliff , here (see below) are the three errors described above with nicer formatting. But that was back in January, so it's probably best to attempt a fresh re-indexing and monitor the output, using cURL or index_current_repo.py.

---

Study ot_232 reports multiple records(?) found, but there's just one JSON with this id in phylesystem-1. This is very similar to a problem discussed in #26:

Indexing http://api.opentreeoflife.org/phylesystem/v1/../ study ot_232 from 
  http://api.opentreeoflife.org/phylesystem/v1/../default/v1/study/ot_232.json
Calling "http://127.0.0.1:7478/db/data/ext/studies/graphdb/index_studies" with 
  data="{'urls': ['http://api.opentreeoflife.org/phylesystem/v1/../default/v1/study/ot_232.json']}"

Indexing failed for 
  URL "http://api.opentreeoflife.org/phylesystem/v1/../default/v1/study/ot_232.json", 
  study http://api.opentreeoflife.org/phylesystem/v1/../default/v1/study/ot_232.json. 
Message = "More than one hit found for ot:studyId == ot_232. The database is probably corrupt."

Two others failed with no explanation:

Indexing http://api.opentreeoflife.org/phylesystem/v1/../ study ot_31 from 
  http://api.opentreeoflife.org/phylesystem/v1/../default/v1/study/ot_31.json
Calling "http://127.0.0.1:7478/db/data/ext/studies/graphdb/index_studies" with
  data="{'urls': ['http://api.opentreeoflife.org/phylesystem/v1/../default/v1/study/ot_31.json']}"

Indexing failed for 
  URL "http://api.opentreeoflife.org/phylesystem/v1/../default/v1/study/ot_31.json", 
  study http://api.opentreeoflife.org/phylesystem/v1/../default/v1/study/ot_31.json. 
Message = "null"

Indexing http://api.opentreeoflife.org/phylesystem/v1/../ study ot_32 from
  http://api.opentreeoflife.org/phylesystem/v1/../default/v1/study/ot_32.json
Calling "http://127.0.0.1:7478/db/data/ext/studies/graphdb/index_studies" with 
  data="{'urls': ['http://api.opentreeoflife.org/phylesystem/v1/../default/v1/study/ot_32.json']}"

Indexing failed for 
  URL "http://api.opentreeoflife.org/phylesystem/v1/../default/v1/study/ot_32.json", 
  study http://api.opentreeoflife.org/phylesystem/v1/../default/v1/study/ot_32.json. 
Message = "null"

[jar398]

This is a major problem, top priority. I'll take a look at it; any help is welcome.

[chinchliff]

There are multiple issues here. For study ot_232, I have no idea why it
would return that error unless there really was already a study indexed
with the same id. Maybe for some reason that study is getting indexed
twice? Maybe one of the other studies has an internal identifier labeling
it at ot_232 even though it is named something else?

The other errors can be retrieved using curl against the devapi OTI. They
are below. Both ot_31 and ot_32 cause OTI to complain that there are leaf
nodes which are not assigned to OTUs. Presuming that this is correct, it
would seem that the solution here would be to fix the nexsons.

I am not sure why those errors are not showing up in the output of the
index_nexsons script. I fixed some of the error reporting code earlier
(neo4j uses the getMessage() method on the exception, if I remember
correctly, so error messages are lost if they are returned any other way),
but maybe I missed something, or maybe those changes haven't been
propagated to api from devapi yet.

---

curl -X POST http://devapi.opentreeoflife.org/v2/studies/index_studies -H
'content-type:application/json' -d '{"urls": ["
http://api.opentreoflife.org/phylesystem/v1/../default/v1/study/ot_31.json
"]}'

{

"message" : "The node Tn295230 is identified as a leaf but has not been
assigned an OTU.",

"exception" : "NexsonParseException",

"fullname" : "org.opentree.nexson.io.NexsonParseException",

"stacktrace" : [
"org.opentree.nexson.io.NexsonNode.parseNexson(NexsonNode.java:235)",
"org.opentree.nexson.io.NexsonNode.(NexsonNode.java:48)",
"org.opentree.nexson.io.NexsonTree.parseNexson(NexsonTree.java:204)",
"org.opentree.nexson.io.NexsonTree.(NexsonTree.java:85)",
"org.opentree.nexson.io.NexsonSource.parseNexson(NexsonSource.java:191)",
"org.opentree.nexson.io.NexsonSource.(NexsonSource.java:52)",
"org.opentree.oti.plugins.studies.readRemoteNexson(studies.java:286)",
"org.opentree.oti.plugins.studies.index_studies(studies.java:189)",
"java.lang.reflect.Method.invoke(Method.java:497)",
"org.neo4j.server.plugins.PluginMethod.invoke(PluginMethod.java:57)",
"org.neo4j.server.plugins.PluginManager.invoke(PluginManager.java:168)",
"org.neo4j.server.rest.web.ExtensionService.invokeGraphDatabaseExtension(ExtensionService.java:300)",
"org.neo4j.server.rest.web.ExtensionService.invokeGraphDatabaseExtension(ExtensionService.java:122)",
"java.lang.reflect.Method.invoke(Method.java:497)",
"org.neo4j.server.rest.security.SecurityFilter.doFilter(SecurityFilter.java:112)"
]

}

curl -X POST http://devapi.opentreeoflife.org/v2/studies/index_studies -H
'content-type:application/json' -d '{"urls": ["
http://api.opentreoflife.org/phylesystem/v1/../default/v1/study/ot_32.json
"]}'

{

"message" : "The node Tn295230 is identified as a leaf but has not been
assigned an OTU.",

"exception" : "NexsonParseException",

"fullname" : "org.opentree.nexson.io.NexsonParseException",

"stacktrace" : [
"org.opentree.nexson.io.NexsonNode.parseNexson(NexsonNode.java:235)",
"org.opentree.nexson.io.NexsonNode.(NexsonNode.java:48)",
"org.opentree.nexson.io.NexsonTree.parseNexson(NexsonTree.java:204)",
"org.opentree.nexson.io.NexsonTree.(NexsonTree.java:85)",
"org.opentree.nexson.io.NexsonSource.parseNexson(NexsonSource.java:191)",
"org.opentree.nexson.io.NexsonSource.(NexsonSource.java:52)",
"org.opentree.oti.plugins.studies.readRemoteNexson(studies.java:286)",
"org.opentree.oti.plugins.studies.index_studies(studies.java:189)",
"java.lang.reflect.Method.invoke(Method.java:497)",
"org.neo4j.server.plugins.PluginMethod.invoke(PluginMethod.java:57)",
"org.neo4j.server.plugins.PluginManager.invoke(PluginManager.java:168)",
"org.neo4j.server.rest.web.ExtensionService.invokeGraphDatabaseExtension(ExtensionService.java:300)",
"org.neo4j.server.rest.web.ExtensionService.invokeGraphDatabaseExtension(ExtensionService.java:122)",
"java.lang.reflect.Method.invoke(Method.java:497)",
"org.neo4j.server.rest.security.SecurityFilter.doFilter(SecurityFilter.java:112)"
]

}

On Wed, Jul 15, 2015 at 12:09 PM Jonathan A Rees notifications@github.com
wrote:

This is a major problem, top priority. I'll take a look at it; any help is
welcome.

—
Reply to this email directly or view it on GitHub
#34 (comment).

[jar398]

Thanks. ot_31 seems to fail the validator. This comes from the treebase converter, so the converter probably needs to change. If it fails to validate I don't know how it got into the repo. I'll copy this to a new peyotl issue.
{
"errors": {
"MISSING_MANDATORY_KEY": {
"data": [
"@otu"
],
"refersTo": {
"@idref": "Tn295377",
"@nodeid": "Tn295377",
"@top": "trees",
"@TreeID": "Tr4206",
"@treesID": "Tb6619"
}
}
},
...

[jar398]

The indexing script is using the ext/studies/graphdb/index_study call,
which probably didn't get updated.

On Wed, Jul 15, 2015 at 3:33 PM, Cody Hinchliff notifications@github.com
wrote:

There are multiple issues here. For study ot_232, I have no idea why it
would return that error unless there really was already a study indexed
with the same id. Maybe for some reason that study is getting indexed
twice? Maybe one of the other studies has an internal identifier labeling
it at ot_232 even though it is named something else?

The other errors can be retrieved using curl against the devapi OTI. They
are below. Both ot_31 and ot_32 cause OTI to complain that there are leaf
nodes which are not assigned to OTUs. Presuming that this is correct, it
would seem that the solution here would be to fix the nexsons.

I am not sure why those errors are not showing up in the output of the
index_nexsons script. I fixed some of the error reporting code earlier
(neo4j uses the getMessage() method on the exception, if I remember
correctly, so error messages are lost if they are returned any other way),
but maybe I missed something, or maybe those changes haven't been
propagated to api from devapi yet.

---

curl -X POST http://devapi.opentreeoflife.org/v2/studies/index_studies -H
'content-type:application/json' -d '{"urls": ["
http://api.opentreoflife.org/phylesystem/v1/../default/v1/study/ot_31.json
"]}'

{

"message" : "The node Tn295230 is identified as a leaf but has not been
assigned an OTU.",

"exception" : "NexsonParseException",

"fullname" : "org.opentree.nexson.io.NexsonParseException",

"stacktrace" : [
"org.opentree.nexson.io.NexsonNode.parseNexson(NexsonNode.java:235)",
"org.opentree.nexson.io.NexsonNode.(NexsonNode.java:48)",
"org.opentree.nexson.io.NexsonTree.parseNexson(NexsonTree.java:204)",
"org.opentree.nexson.io.NexsonTree.(NexsonTree.java:85)",
"org.opentree.nexson.io.NexsonSource.parseNexson(NexsonSource.java:191)",
"org.opentree.nexson.io.NexsonSource.(NexsonSource.java:52)",
"org.opentree.oti.plugins.studies.readRemoteNexson(studies.java:286)",
"org.opentree.oti.plugins.studies.index_studies(studies.java:189)",
"java.lang.reflect.Method.invoke(Method.java:497)",
"org.neo4j.server.plugins.PluginMethod.invoke(PluginMethod.java:57)",
"org.neo4j.server.plugins.PluginManager.invoke(PluginManager.java:168)",

"org.neo4j.server.rest.web.ExtensionService.invokeGraphDatabaseExtension(ExtensionService.java:300)",

"org.neo4j.server.rest.web.ExtensionService.invokeGraphDatabaseExtension(ExtensionService.java:122)",
"java.lang.reflect.Method.invoke(Method.java:497)",

"org.neo4j.server.rest.security.SecurityFilter.doFilter(SecurityFilter.java:112)"
]

}

curl -X POST http://devapi.opentreeoflife.org/v2/studies/index_studies -H
'content-type:application/json' -d '{"urls": ["
http://api.opentreoflife.org/phylesystem/v1/../default/v1/study/ot_32.json
"]}'

{

"message" : "The node Tn295230 is identified as a leaf but has not been
assigned an OTU.",

"exception" : "NexsonParseException",

"fullname" : "org.opentree.nexson.io.NexsonParseException",

"stacktrace" : [
"org.opentree.nexson.io.NexsonNode.parseNexson(NexsonNode.java:235)",
"org.opentree.nexson.io.NexsonNode.(NexsonNode.java:48)",
"org.opentree.nexson.io.NexsonTree.parseNexson(NexsonTree.java:204)",
"org.opentree.nexson.io.NexsonTree.(NexsonTree.java:85)",
"org.opentree.nexson.io.NexsonSource.parseNexson(NexsonSource.java:191)",
"org.opentree.nexson.io.NexsonSource.(NexsonSource.java:52)",
"org.opentree.oti.plugins.studies.readRemoteNexson(studies.java:286)",
"org.opentree.oti.plugins.studies.index_studies(studies.java:189)",
"java.lang.reflect.Method.invoke(Method.java:497)",
"org.neo4j.server.plugins.PluginMethod.invoke(PluginMethod.java:57)",
"org.neo4j.server.plugins.PluginManager.invoke(PluginManager.java:168)",

"org.neo4j.server.rest.web.ExtensionService.invokeGraphDatabaseExtension(ExtensionService.java:300)",

"org.neo4j.server.rest.web.ExtensionService.invokeGraphDatabaseExtension(ExtensionService.java:122)",
"java.lang.reflect.Method.invoke(Method.java:497)",

"org.neo4j.server.rest.security.SecurityFilter.doFilter(SecurityFilter.java:112)"
]

}

On Wed, Jul 15, 2015 at 12:09 PM Jonathan A Rees <notifications@github.com

wrote:

This is a major problem, top priority. I'll take a look at it; any help
is
welcome.

—
Reply to this email directly or view it on GitHub
<#34 (comment)
.

—
Reply to this email directly or view it on GitHub
#34 (comment).